ℙrediction models of five brain region gene expression in rats. See description in Santhanam, Sanchez Roige, et al (2024). Download link To query the database, checkout this post […] Natasha Santhanam, Sandra Sanchez-Roige, Yanyu Liang, Apurva S. Chitre, Daniel Munro, Denghui Chen, Riyan … Read more →

𝕎e downloaded the pathogenicity predictions from Alpha-Missense and made this shinyapp to query. Try it out. https://imlab.shinyapps.io/alphamissense-query-hugo/ Jun Cheng et al., Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 381 (2023) … Read more →

𝔻ownload prediction weights from: https://zenodo.org/record/7551845#.Y_5QTLTMIqs Preprint from Wheeler lab sharing multi-ancestry prediction models from TOPMED/MESA https://www.biorxiv.org/content/10.1101/2023.02.09.527747v1 […] Multivariate adaptive shrinkage improves cross-population … Read more →

𝔽ind the mapping from intron ids to gene ids in this link https://uchicago.box.com/s/xy71r0su6refrfggivrwc7kpvsxysmmn […] Q: How should I interpret the z-score? Does a negative z-score for an intron imply that a decrease in the excision of that intron leads to an increase in the GWAS trait? … Read more →

𝔸RIC protein prediction models in predictdb format can be downloaded from here https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc See more details here https://lab-notes.hakyimlab.org/post/2021/09/08/generating-metaxcan-prediction-model-from-aric-pwas/ Read more →

𝕋he MetaXcan Software hosts a suite of tools i.e PrediXcan, SPrediXcan, MultiXcan and SMultiXcan. This post describes the file format output from each tool. […] Individual-level data method to compute gene-trait associations. Detailed info The output is a tab delimited file which contains … Read more →

ℙrediXcan ready databases and covariance files of the paper “Protein prediction for trait mapping in diverse populations” can be downloaded from here https://doi.org/10.5281/zenodo.4837327 Read more →

𝕆ne step of the summary imputation, the computation of snp covariance matrix inverse, is performed via singular value decomposition (SVD). Numerical solutions to the SVD algorithm are not guaranteed to converge, and fail on some regions. When this happens, unmeasured zscores will not be present in … Read more →

𝕋his error happen when the strings captured from the metaxcan results and models don’t coincide A good example is when the metaxcan results' captured names looked like Aorta while the models' captured names looked like Artery_Aorta, this will result into this error […] … Read more →

𝕊-BrainXcan takes GWAS as input and return the association between GWAS phenotype and a list of brain image-derived phenotypes. BrainXcan manuscript link. Software documentation (Quick start) link. BrainXcan database link. Analysis scripts link. […] The software is built upon both Python and … Read more →